Browsing by Subject "genome annotation"

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  • Vaattovaara, Aleksia Fanni Maria; Leppälä, Johanna Maria; Salojärvi, Jarkko Tapani; Wrzaczek, Michael Alois (2019)
    The use of draft genomes of different species and re-sequencing of accessions and populations are now a common tool for plant biology research. The de novo assembled draft genomes make it possible to identify pivotal divergence points in the plant lineage and provide an opportunity to investigate the genomic basis and timing of biological innovations by inferring orthologs between species. Furthermore, re-sequencing facilitates the mapping and subsequent molecular characterization of causative loci for traits including plant stress tolerance or development. In both cases high quality gene annotation, the identification of protein-coding regions, gene promoters and 5’ and 3’ untranslated regions, is critical for investigation of gene function. Annotations are constantly improving but automated gene annotations still require manual curation and experimental validation. This is particularly important for genes with large introns, genes located in regions rich with transposable elements or repeats, large gene families and segmentally duplicated genes. In this opinion paper we highlight the impact of annotation quality on evolutionary analyses, genome-wide association studies and the identification of orthologous genes in plants. Furthermore, we predict that incorporating the accurate information from manual curation into databases will dramatically improve the performance of automated gene predictors.
  • Elbers, Jean P.; Rogers, Mark F.; Perelman, Polina L.; Proskuryakova, Anastasia A.; Serdyukova, Natalia A.; Johnson, Warren E.; Horin, Petr; Corander, Jukka; Murphy, David; Burger, Pamela A. (2019)
    Researchers have assembled thousands of eukaryotic genomes using Illumina reads, but traditional mate-pair libraries cannot span all repetitive elements, resulting in highly fragmented assemblies. However, both chromosome conformation capture techniques, such as Hi-C and Dovetail Genomics Chicago libraries and long-read sequencing, such as Pacific Biosciences and Oxford Nanopore, help span and resolve repetitive regions and therefore improve genome assemblies. One important livestock species of arid regions that does not have a high-quality contiguous reference genome is the dromedary (Camelus dromedarius). Draft genomes exist but are highly fragmented, and a high-quality reference genome is needed to understand adaptation to desert environments and artificial selection during domestication. Dromedaries are among the last livestock species to have been domesticated, and together with wild and domestic Bactrian camels, they are the only representatives of the Camelini tribe, which highlights their evolutionary significance. Here we describe our efforts to improve the North African dromedary genome. We used Chicago and Hi-C sequencing libraries from Dovetail Genomics to resolve the order of previously assembled contigs, producing almost chromosome-level scaffolds. Remaining gaps were filled with Pacific Biosciences long reads, and then scaffolds were comparatively mapped to chromosomes. Long reads added 99.32 Mbp to the total length of the new assembly. Dovetail Chicago and Hi-C libraries increased the longest scaffold over 12-fold, from 9.71 Mbp to 124.99 Mbp and the scaffold N50 over 50-fold, from 1.48 Mbp to 75.02 Mbp. We demonstrate that Illumina de novo assemblies can be substantially upgraded by combining chromosome conformation capture and long-read sequencing.
  • Lonardi, Stefano; Muñoz-Amatriaín, María; Liang, Qihua; Shu, Shengqiang; Wanamaker, Steve I.; Lo, Sassoum; Tanskanen, Jaakko; Schulman, Alan H.; Zhu, Tingting; Luo, Ming-Cheng; Alhakami, Hind; Ounit, Rachid; Hasan, Abid Md.; Verdier, Jerome; Roberts, Philip A.; Santos, Jansen R.P.; Ndeve, Arsenio; Doležel, Jaroslav; Vrána, Jan; Hokin, Samuel A.; Farmer, Andrew D.; Cannon, Steven B.; Close, Timothy J. (2019)
    Cowpea (Vigna unguiculata [L.] Walp.) is a major crop for worldwide food and nutritional security, especially in sub-Saharan Africa, that is resilient to hot and drought-prone environments. An assembly of the single-haplotype inbred genome of cowpea IT97K-499-35 was developed by exploiting the synergies between single-molecule real-time sequencing, optical and genetic mapping, and an assembly reconciliation algorithm. A total of 519 Mb is included in the assembled sequences. Nearly half of the assembled sequence is composed of repetitive elements, which are enriched within recombination-poor pericentromeric regions. A comparative analysis of these elements suggests that genome size differences between Vigna species are mainly attributable to changes in the amount of Gypsy retrotransposons. Conversely, genes are more abundant in more distal, high-recombination regions of the chromosomes; there appears to be more duplication of genes within the NBS-LRR and the SAUR-like auxin superfamilies compared with other warm-season legumes that have been sequenced. A surprising outcome is the identification of an inversion of 4.2 Mb among landraces and cultivars, which includes a gene that has been associated in other plants with interactions with the parasitic weed Striga gesnerioides. The genome sequence facilitated the identification of a putative syntelog for multiple organ gigantism in legumes. A revised numbering system has been adopted for cowpea chromosomes based on synteny with common bean (Phaseolus vulgaris). An estimate of nuclear genome size of 640.6 Mbp based on cytometry is presented.